I have two bed files with 4 columns each and I'd like to intersect the bed files, then carry over the 4th column of one of the files as the 4th column of the result.
depth.bed
, an output file from mosdepth, has very short intervals (from 1bp to ~200bp each).
exons.bed
is a regular BED file with exon coordinates
When I tried bedtools intersect -a depth.bed -b exons.bed
, there was no result as (I'm guessing) bedtools expect -a
to be the file with the large intervals. I flipped the inputs and used bedtools intersect -a exons.bed -b depth.bed
and this time, it worked fine.
However, the output now has the 4th column from exons.bed
whereas I need the 4th column from depth.bed
. I added the -wb
option to get that included but what happens now is that I get the 4th column from exons.bed
AND all 4 columns from depth.bed
. I can use cut
or awk
to get just the columns I need, but is there any way to ask bedtools to give me just depth.bed
's 4th column without adding a bunch of other stuff? Essentially, can I annotate my damn BED file with one column from another bed file?
You're right. Maybe I made a typo or some other stupid mistake that caused my command to exit without any error or output.
Swapping the
-a
and-b
solves the overall problem too, as the last field is picked from-a
file by default. Thank you!